The Experts below are selected from a list of 145293 Experts worldwide ranked by ideXlab platform
Yan Yan - One of the best experts on this subject based on the ideXlab platform.
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crystal structure of sars cov 2 nucleocapsid Protein RNA Binding domain reveals potential unique drug targeting sites
Acta Pharmaceutica Sinica B, 2020Co-Authors: Sisi Kang, Mei Yang, Zhongsi Hong, Liping Zhang, Zhaoxia Huang, Xiaoxue Chen, Ziliang Zhou, Zhechong Zhou, Qiuyue Chen, Yan YanAbstract:Abstract The outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. Currently, there is no specific viral Protein-targeted therapeutics. Viral nucleocapsid Protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid Protein remains unclear. Herein, we have determined the 2.7 A crystal structure of the N-terminal RNA Binding domain of SARS-CoV-2 nucleocapsid Protein. Although the overall structure is similar as other reported coronavirus nucleocapsid Protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA Binding pocket alongside the β-sheet core. Complemented by in vitro Binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid Protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.
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crystal structure of sars cov 2 nucleocapsid Protein RNA Binding domain reveals potential unique drug targeting sites
bioRxiv, 2020Co-Authors: Sisi Kang, Mei Yang, Zhongsi Hong, Liping Zhang, Zhaoxia Huang, Xiaoxue Chen, Ziliang Zhou, Zhechong Zhou, Qiuyue Chen, Yan YanAbstract:Abstract The outbreak of coronavirus disease (COVID-19) in China caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. It is currently no specific viral Protein targeted therapeutics yet. Viral nucleocapsid Protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid Protein is yet to be clear. Herein, we have determined the 2.7 A crystal structure of the N-terminal RNA Binding domain of SARS-CoV-2 nucleocapsid Protein. Although overall structure is similar with other reported coronavirus nucleocapsid Protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA Binding pocket alongside the β-sheet core. Complemented by in vitro Binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid Protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.
Jean-christophe Giard - One of the best experts on this subject based on the ideXlab platform.
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Cold-shock RNA-Binding Protein CspR is also exposed to the surface of Enterococcus faecalis
Microbiology, 2013Co-Authors: Charlotte Michaux, Axel Hartke, Nicolas Verneuil, Luis Felipe Romero Saavedra, Fanny Reffuveille, Benoît Bernay, Didier Goux, Jean-christophe GiardAbstract:CspR has been characterized recently as a cold-shock RNA-Binding Protein in Enterococcus faecalis, a natural member of the gastro-intestinal tract capable of switching from a commensal relationship with the host to an important nosocomial pathogen. In addition to its involvement in the cold-shock response, CspR also plays a role in the long-term survival and virulence of E. faecalis. In the present study, we demonstrated that anti-CspR immune rabbit serum protected larvae of Galleria mellonella against a lethal challenge of the WT strain. These results suggested that CspR might have a surface location. This hypothesis was verified by Western blot that showed detection of CspR in the total as well as in the surface Protein fraction. In addition, identification of surface polypeptides by proteolytic shaving of intact bacterial cells followed by liquid chromatography-MS-MS revealed that cold-shock Proteins (EF1367, EF2939 and CspR) were present on the cell surface. Lastly, anti-CspR immune rabbit serum was used for immunolabelling and detected with colloidal gold-labelled goat anti-rabbit IgG in order to determine the immunolocalization of CspR on E. faecalis WT strain. Electron microscopy images confirmed that the cold-shock Protein RNA-Binding Protein CspR was present in both cytoplasmic and surface parts of the cell. These data strongly suggest that CspR, in addition to being located intracellularly, is also present in the extracellular Protein fraction of the cells and has important functions in the infection process of Galleria larvae.
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CspR, a Cold Shock RNA-Binding Protein Involved in the Long-Term Survival and the Virulence of Enterococcus faecalis
Journal of Bacteriology, 2012Co-Authors: Charlotte Michaux, Cecilia Martini, Koki Shioya, Sandra Ahmed Lecheheb, Aurélie Budin-verneuil, Pascal Cosette, Maurizio Sanguinetti, Axel Hartke, Nicolas Verneuil, Jean-christophe GiardAbstract:By coprecipitation, we identified RNA-Binding Proteins in the Gram-positive opportunistic pathogen Enterococcus faecalis known to be deficient of the RNA chaperone Hfq. In particular, we characterized one belonging to the cold shock Protein (Csp) family (Ef2925) renamed CspR for cold shock Protein RNA Binding. Compared to the wild-type strain, the ΔcspR mutant was less virulent in an insect infection model (Galleria mellonella) and exhibited a decreased persistence in mouse kidneys and a low survival rate in peritoneal macrophages. As expected, we found that the ΔcspR mutant strain was more impaired in its growth than the parental strain under cold conditions and in its long-term survival under nutrient starvation. All these phenotypes were restored after complementation of the ΔcspR mutant. In addition, Western blot analysis showed that CspR was overexpressed under cold shock conditions and in the stationary phase. Since CspR may act as an RNA chaperone, putative targets were identified using a global proteomic approach completed with transcriptomic assays. This study revealed that 19 Proteins were differentially expressed in the ΔcspR strain (9 upregulated, 10 downregulated) and that CspR mainly acted at the posttranscriptional level. These data highlight for the first time the role of the RNA-Binding Protein CspR as a regulator in E. faecalis and its requirement in stress response and virulence in this important human pathogen.
Taihuang Huang - One of the best experts on this subject based on the ideXlab platform.
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structure of the sars coronavirus nucleocapsid Protein RNA Binding dimerization domain suggests a mechanism for helical packaging of viral RNA
Journal of Molecular Biology, 2007Co-Authors: Chunyuan Chen, Chung Ke Chang, Yiwei Chang, Shih Che Sue, Hsin I Bai, Lilianty Riang, Chwandeng Hsiao, Taihuang HuangAbstract:Coronavirus nucleocapsid Proteins are basic Proteins that encapsulate viral genomic RNA to form part of the virus structure. The nucleocapsid Protein of SARS-CoV is highly antigenic and associated with several host-cell interactions. Our previous studies using nuclear magnetic resonance revealed the domain organization of the SARS-CoV nucleocapsid Protein. RNA has been shown to bind to the N-terminal domain (NTD), although recently the C-terminal half of the Protein has also been implicated in RNA Binding. Here, we report that the C-terminal domain (CTD), spanning residues 248-365 (NP248-365), had stronger nucleic acid-Binding activity than the NTD. To determine the molecular basis of this activity, we have also solved the crystal structure of the NP248-365 region. Residues 248-280 form a positively charged groove similar to that found in the infectious bronchitis virus (IBV) nucleocapsid Protein. Furthermore, the positively charged surface area is larger in the SARS-CoV construct than in the IBV. Interactions between residues 248-280 and the rest of the molecule also stabilize the formation of an octamer in the asymmetric unit. Packing of the octamers in the crystal forms two parallel, basic helical grooves, which may be oligonucleotide attachment sites, and suggests a mechanism for helical RNA packaging in the virus.
Peter Freese - One of the best experts on this subject based on the ideXlab platform.
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Allele-specific Binding of RNA-Binding Proteins reveals functional genetic variants in the RNA.
Nature Communications, 2019Co-Authors: Ei-wen Yang, Jae Hoon Bahn, Esther Yun-hua Hsiao, Boon Xin Tan, Yiwei Sun, Bo Zhou, Eric L. Van Nostrand, Gabriel A. Pratt, Peter FreeseAbstract:Allele-specific Protein-RNA Binding is an essential aspect that may reveal functional genetic variants (GVs) mediating post-transcriptional regulation. Recently, genome-wide detection of in vivo Binding of RNA-Binding Proteins is greatly facilitated by the enhanced crosslinking and immunoprecipitation (eCLIP) method. We developed a new computational approach, called BEAPR, to identify allele-specific Binding (ASB) events in eCLIP-Seq data. BEAPR takes into account crosslinking-induced sequence propensity and variations between replicated experiments. Using simulated and actual data, we show that BEAPR largely outperforms often-used count analysis methods. Importantly, BEAPR overcomes the inherent overdispersion problem of these methods. Complemented by experimental validations, we demonstrate that the application of BEAPR to ENCODE eCLIP-Seq data of 154 Proteins helps to predict functional GVs that alter splicing or mRNA abundance. Moreover, many GVs with ASB patterns have known disease relevance. Overall, BEAPR is an effective method that helps to address the outstanding challenge of functional interpretation of GVs.
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allele specific Binding of RNA Binding Proteins reveals functional genetic variants in the RNA
bioRxiv, 2018Co-Authors: Ei-wen Yang, Jae Hoon Bahn, Esther Yun-hua Hsiao, Boon Xin Tan, Yiwei Sun, Bo Zhou, Eric L. Van Nostrand, Gabriel A. Pratt, Peter Freese, Xintao WeiAbstract:Allele-specific Protein-RNA Binding is an essential aspect that may reveal functional genetic variants influencing RNA processing and gene expression phenotypes. Recently, genome-wide detection of in vivo Binding sites of RNA Binding Proteins (RBPs) is greatly facilitated by the enhanced UV crosslinking and immunoprecipitation (eCLIP) protocol. Hundreds of eCLIP-Seq data sets were generated from HepG2 and K562 cells during the ENCODE3 phase. These data afford a valuable opportunity to examine allele-specific Binding (ASB) of RBPs. To this end, we developed a new computational algorithm, called BEAPR (Binding Estimation of Allele-specific Protein-RNA interaction). In identifying statistically significant ASB sites, BEAPR takes into account UV cross-linking induced sequence propensity and technical variations between replicated experiments. Using simulated data and actual eCLIP-Seq data, we show that BEAPR largely outperforms often-used methods Chi-Squared test and Fisher9s Exact test. Importantly, BEAPR overcomes the inherent over-dispersion problem of the other methods. Complemented by experimental validations, we demonstrate that ASB events are significantly associated with genetic regulation of splicing and mRNA abundance, supporting the usage of this method to pinpoint functional genetic variants in post-transcriptional gene regulation. Many variants with ASB patterns of RBPs were found as genetic variants with cancer or other disease relevance. About 38% of ASB variants were in linkage disequilibrium with single nucleotide polymorphisms from genome-wide association studies. Overall, our results suggest that BEAPR is an effective method to reveal ASB patterns in eCLIP and can inform functional interpretation of disease-related genetic variants.
Sisi Kang - One of the best experts on this subject based on the ideXlab platform.
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crystal structure of sars cov 2 nucleocapsid Protein RNA Binding domain reveals potential unique drug targeting sites
Acta Pharmaceutica Sinica B, 2020Co-Authors: Sisi Kang, Mei Yang, Zhongsi Hong, Liping Zhang, Zhaoxia Huang, Xiaoxue Chen, Ziliang Zhou, Zhechong Zhou, Qiuyue Chen, Yan YanAbstract:Abstract The outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. Currently, there is no specific viral Protein-targeted therapeutics. Viral nucleocapsid Protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid Protein remains unclear. Herein, we have determined the 2.7 A crystal structure of the N-terminal RNA Binding domain of SARS-CoV-2 nucleocapsid Protein. Although the overall structure is similar as other reported coronavirus nucleocapsid Protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA Binding pocket alongside the β-sheet core. Complemented by in vitro Binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid Protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.
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crystal structure of sars cov 2 nucleocapsid Protein RNA Binding domain reveals potential unique drug targeting sites
bioRxiv, 2020Co-Authors: Sisi Kang, Mei Yang, Zhongsi Hong, Liping Zhang, Zhaoxia Huang, Xiaoxue Chen, Ziliang Zhou, Zhechong Zhou, Qiuyue Chen, Yan YanAbstract:Abstract The outbreak of coronavirus disease (COVID-19) in China caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. It is currently no specific viral Protein targeted therapeutics yet. Viral nucleocapsid Protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid Protein is yet to be clear. Herein, we have determined the 2.7 A crystal structure of the N-terminal RNA Binding domain of SARS-CoV-2 nucleocapsid Protein. Although overall structure is similar with other reported coronavirus nucleocapsid Protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA Binding pocket alongside the β-sheet core. Complemented by in vitro Binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid Protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.
